Cold water pollution (CWP), the discharge of cold hypolimnetic water from large dams, is a widespread stressor of regulated rivers, yet its effects on fish communities are documented almost entirely for large-bodied fishes. Small-bodied native species with short, near-annual life cycles depend on regular temperature-cued spawning and rapid recruitment to persist. We quantified thermal spawning opportunity for small-bodied native species in two CWP-affected rivers (the Severn River, downstream of Pindari Dam; the Gwydir River, downstream of Copeton Dam) and an unimpacted reference (Mole River) in Australia’s northern Murray–Darling Basin and assessed the small-bodied native fish community in the same systems. Spawning-suitable days were markedly reduced below both dams and this suppression persisted across 13 years in the Severn River (e.g. hardyhead spp.: median 4 days versus 110 days annually). The reference river supported six small-bodied native taxa; the CWP-affected Gwydir River retained five species but lower catch rates, and the Severn retained a single taxon (carp gudgeon spp.). We identify short-lived small-bodied natives as sensitive sentinels of CWP whose persistence may depend on tributary refugia and nearby source populations. Additionally, findings highlight the need to extend CWP assessment beyond large-bodied species.